Dear Amber developers,
Thank you for usual kind support.
I am now trying to calculate energy component by using sander on Amber11.
Energy calculation was done and proper values were obtained.
But I just worry whether obtained energy values were really those derived
from the input snapshots,
Thus, not the energy derived from minimized structures.
Amber11 manual says in p26
"If maxcyc=1, then the output file can be
used to extract the energies of each of the coordinate sets in the inptraj
file."
And I follow that.
While in my sander output, I found the statements:
"Maximum number of minimization cycles reached."
and the following calculation logs
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -9.8754E+03 1.2450E+01 6.5958E+01 NH2 1744
BOND = 0.0000 ANGLE = 2318.2691 DIHED = 3019.2679
VDWAALS = -2244.5840 EEL = -22758.6673 EGB = -2679.6571
1-4 VDW = 1075.6518 1-4 EEL = 11320.3164 RESTRAINT = 0.0000
ESURF = 74.0312
Do I need not to worry about these sentences and believe I obtained the
expected information on energy?
Or I need to set additional parameter (e.g. avoiding MINIMIZATION PROCESS)
to achieve what I want to know?
I am most grateful if you give me some advices.
Yours sincerely,
Ikuo KURISAKI
PS
In my input file, imin, maxcyc and idecomp were set as 5, 1, 2,
respectively,
And the following mdin file was used.
#decompose energy on a per-residue basis on the trajectory
&cntrl
imin = 5, igb = 5, gbsa = 2, rgbmax = 8.21,
ntx = 1, maxcyc = 1,
ntc = 2, ntf = 2,
ntb = 0, ntp = 0,
ntwe = 0, ntpr = 500, ntwx=1,
cut = 9, idecomp = 2,
/
Residues considered as REC
RRES 1 295
END
Residues considered as LIG
LRES 296 296
END
Residues to print
RES 1 295
END
END
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Received on Mon Oct 17 2011 - 00:00:03 PDT
